I'm not familiar with GIMP, but in Paint Shop Pro I have to run the optimizer while saving to get a transparency to stick. So, I "Save As", click "Options", and then click "Run Optimizer". If everything looks right, then I save in the optimizer.
There may be an easier way to do it, but I don't deal with transparencies all that often so it's not a big deal to me to take a couple of extra steps.
ETA: Good to know about resizing.